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1.
J Mater Chem B ; 12(16): 4004-4017, 2024 Apr 24.
Article in English | MEDLINE | ID: mdl-38568714

ABSTRACT

Melatonin (MT) is a vital hormone controlling biorhythms, and optimizing its release in the human body is crucial. To address MT's unfavorable pharmacokinetics, we explored the inclusion complexes of MT with ß-cyclodextrin (ß-CD). Nano spray drying was applied to efficiently synthesize these complexes in three molar ratios (MT : ß-CD = 1 : 1, 2 : 1, and 1 : 2), reducing reagent use and expediting inclusion. The complex powders were characterized through thermal analyses (TGA and DSC), Fourier transform infrared spectroscopy (FTIR), and in vitro MT release measurements via high-performance liquid chromatography (HPLC). In parallel, computational studies were conducted, examining the stability of MT : ß-CD complexes by means of unbiased semi-empirical conformational searches refined by DFT, which produced a distribution of MT : ß-CD binding enthalpies. Computational findings highlighted that these complexes are stabilized by specific hydrogen bonds and non-specific dispersive forces, with stronger binding in the 1 : 1 complex, which was corroborated by in vitro release data. Furthermore, the alignment between simulated and experimental FTIR spectra demonstrated the quality of both the structural model and computational methodology, which was crucial to enhance our comprehension of optimizing MT's release for therapeutic applications.


Subject(s)
Melatonin , beta-Cyclodextrins , beta-Cyclodextrins/chemistry , Melatonin/chemistry , Density Functional Theory , Drug Liberation , Spectroscopy, Fourier Transform Infrared
2.
RSC Adv ; 14(17): 12038-12048, 2024 Apr 10.
Article in English | MEDLINE | ID: mdl-38623301

ABSTRACT

The hexagonal structure of LiBH4 at room temperature can be stabilised by substituting the BH4- anion with I-, leading to high Li-ion conductive materials. A thermodynamic description of the pseudo-binary LiBH4-LiI system is presented. The system has been explored investigating several compositions, synthetized by ball milling and subsequently annealed. X-ray diffraction and Differential Scanning Calorimetry have been exploited to determine structural and thermodynamic features of various samples. The monophasic zone of the hexagonal Li(BH4)1-x(I)x solid solution has been experimentally defined equal to 0.18 ≤ x ≤ 0.60 at 25 °C. In order to establish the formation of the hexagonal solid solution, the enthalpy of mixing was experimentally determined, converging to a value of 1800 ± 410 J mol-1. Additionally, the enthalpy of melting was acquired for samples that differ in molar fraction. By merging experimental results, literature data and ab initio theoretical calculations, the pseudo-binary LiBH4-LiI phase diagram has been assessed and evaluated across all compositions and temperature ranges by applying the CALPHAD method.

3.
RSC Adv ; 14(9): 6398-6409, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38380234

ABSTRACT

The energetic transition towards renewable resources is one of the biggest challenges of this century. In this context, the role of H2 is of paramount importance as a key source of energy that could substitute traditional fossil fuels. This technology, even if available in several manufactures, still needs to be optimized at all levels (production, storage and distribution) to be integrated on a larger scale. Among materials suitable to store H2, Mg(BH4)2 is particularly interesting due to its high content of H2 in terms of gravimetric density. Nanosizing effects and role of additives in the decomposition of Mg(BH4)2 were studied by density functional theory (DFT) modelling. Both effects were analyzed because of their contribution in promoting the decomposition of the material. In particular, to have a quantitative idea of nanosizing effects, we used thin film 2D models corresponding to different crystallographic surfaces and referred to the following reaction: Mg(BH4)2 → MgB2 + 4H2. When moving from bulk to nanoscale (2D models), a remarkable decrease in the decomposition energy (10-20 kJ mol-1) was predicted depending on the surface and the thin film thickness considered. As regards the role of additives (Ni and Cu), we based our analysis on their effect in perturbing neighboring borohydride groups. We found a clear elongation of some B-H bonds, in particular with the NiF2 additive (about 0.1 Å). We interpreted this behavior as an indicator of the propensity of borohydride towards dissociation. On the basis of this evidence, we also explored a possible reaction pathway of NiF2 and CuF2 on Mg(BH4)2 up to H2 release and pointed out the major catalytic effect of Ni compared to Cu.

4.
Int J Mol Sci ; 24(23)2023 Nov 27.
Article in English | MEDLINE | ID: mdl-38069149

ABSTRACT

Cyclodextrins (CDs) constitute a class of cyclic oligosaccharides that are well recognized and largely applied in the drug delivery field, thanks to their biocompatibility, low cost, and the possibility to be derivatized in order to tune and optimize the complexation/release of the specific drug. The conformational flexibility of these systems is one of their key properties and requires a cost-effective methodology to be studied by combining the accuracy of results with the possibility of exploring a large set of conformations. In the present paper, we have explored the conformational potential energy surface of the monomers and dimers of α-, ß-, and γ-cyclodextrins (i.e., 6, 7, and 8 monomeric units, respectively) by means of fast but accurate semiempirical methods, which are then refined by state-of-the-art DFT functionals. Moreover, the crystal structure is considered for a more suitable comparison with the IR spectrum experimentally recorded. Calculations are carried out in the gas phase and in water environments, applying both implicit and explicit treatments. We show that the conformation of the studied molecules changes from the gas phase to the water, even if treated implicitly, thus modifying their complexation capability.


Subject(s)
Cyclodextrins , gamma-Cyclodextrins , Models, Molecular , Cyclodextrins/chemistry , Molecular Conformation , Water/chemistry
5.
ACS Earth Space Chem ; 7(10): 2050-2061, 2023 Oct 19.
Article in English | MEDLINE | ID: mdl-37876665

ABSTRACT

Phosphorus (P) is a fundamental element for whatever form of life, in the same way as the other biogenic macroelements (SONCH). The prebiotic origin of P is still a matter of debate, as the phosphates present on earth are trapped in almost insoluble solid matrixes (apatites) and, therefore, hardly available for inclusion in living systems in the prebiotic era. The most accepted theories regard a possible exogenous origin during the Archean Era, through the meteoritic bombardment, when tons of reactive P in the form of phosphide ((Fe,Ni)3P, schreibersite mineral) reached the primordial earth, reacting with water and providing oxygenated phosphorus compounds (including phosphates). In the last 20 years, laboratory experiments demonstrated that the corrosion process of schreibersite by water indeed leads to reactive phosphates that, in turn, react with other biological building blocks (nucleosides and simple sugars) to form more complex molecules (nucleotides and complex sugars). In the present paper, we study the water corrosion of different crystalline surfaces of schreibersite by means of periodic DFT (density functional theory) simulations. Our results show that water adsorbs molecularly on the most stable (110) surface but dissociates on the less stable (001) one, giving rise to further reactivity. Indeed, subsequent water adsorptions, up to the water monolayer coverage, show that, on the (001) surface, iron and nickel atoms are the first species undergoing the corrosion process and, in a second stage, the phosphorus atoms also get involved. When adsorbing up to three and four water molecules per unit cell, the most stable structures found are the phosphite and phosphate forms of phosphorus, respectively. Simulation of the vibrational spectra of the considered reaction products revealed that the experimental band at 2423 cm-1 attributed to the P-H stretching frequency is indeed predicted for a phosphite moiety attached to the schreibersite (001) surface upon chemisorption of up to three water molecules.

6.
Phys Chem Chem Phys ; 25(39): 26797-26812, 2023 Oct 11.
Article in English | MEDLINE | ID: mdl-37781958

ABSTRACT

Hydrogen cyanide (HCN) represents a small but widely distributed fraction of the interstellar molecules, and it has been observed in all the environments characterizing the formation of a new planetary system. HCN can polymerize to form biomolecules, including adenine (H5C5N5), and it has drawn attention as a possible precursor of several building blocks of life due to the presence of its polymerization products in meteorites, comets and other asteroidal bodies. To elucidate the potential catalytic role that cosmic silicates have played in these processes, we have investigated, at DFT-PBE level inclusive of a posteriori dispersion correction, the energetic and spectroscopic features of the adsorption of HCN molecules on the most relevant crystalline surfaces of the mineral forsterite (Mg2SiO4), a common silicate constituent of the interstellar core grains and planetary rocky bodies. The results reveal that HCN adsorbs both in molecular and dissociative ways, within a wide range of adsorption energies (-29.4 to -466.4 kJ mol-1). Thermodynamic and kinetic results show that dissociative adsorption is dominant already at low temperatures, a fact particularly relevant at the protoplanetary conditions (i.e., the latest stages in the star system formation process). The simulated spectroscopic features of the studied adducts show a wide range of different degrees of perturbation of C-H and CN bonds. This finding agrees with previous experimental works, and our results confirm that a complex chemistry is observed when this astrochemically-relevant molecule interacts with Mg2SiO4, which may be associated with a considerable potential reactivity towards the formation of relevant prebiotic compounds.

7.
Polymers (Basel) ; 15(6)2023 Mar 20.
Article in English | MEDLINE | ID: mdl-36987322

ABSTRACT

Melatonin is a neurohormone that ameliorates many health conditions when it is administered as a drug, but its drawbacks are its oral and intravenous fast release. To overcome the limitations associated with melatonin release, cyclodextrin-based nanosponges (CD-based NSs) can be used. Under their attractive properties, CD-based NSs are well-known to provide the sustained release of the drug. Green cyclodextrin (CD)-based molecularly imprinted nanosponges (MIP-NSs) are successfully synthesized by reacting ß-Cyclodextrin (ß-CD) or Methyl-ß Cyclodextrin (M-ßCD) with citric acid as a cross-linking agent at a 1:8 molar ratio, and melatonin is introduced as a template molecule. In addition, CD-based non-molecularly imprinted nanosponges (NIP-NSs) are synthesized following the same procedure as MIP-NSs without the presence of melatonin. The resulting polymers are characterized by CHNS-O Elemental, Fourier Transform Infrared Spectroscopy (FTIR), Thermogravimetric (TGA), Differential Scanning Calorimetry (DSC), Zeta Potential, and High-Performance Liquid Chromatography (HPLC-UV) analyses, etc. The encapsulation efficiencies are 60-90% for MIP-NSs and 20-40% for NIP-NSs, whereas melatonin loading capacities are 1-1.5% for MIP-NSs and 4-7% for NIP-NSs. A better-controlled drug release performance (pH = 7.4) for 24 h is displayed by the in vitro release study of MIP-NSs (30-50% released melatonin) than NIP-NSs (50-70% released melatonin) due to the different associations within the polymeric structure. Furthermore, a computational study, through the static simulations in the gas phase at a Geometry Frequency Non-covalent interactions (GFN2 level), is performed to support the inclusion complex between ßCD and melatonin with the automatic energy exploration performed by Conformer-Rotamer Ensemble Sampling Tool (CREST). A total of 58% of the CD/melatonin interactions are dominated by weak forces. CD-based MIP-NSs and CD-based NIP-NSs are mixed with cream formulations for enhancing and sustaining the melatonin delivery into the skin. The efficiency of cream formulations is determined by stability, spreadability, viscosity, and pH. This development of a new skin formulation, based on an imprinting approach, will be of the utmost importance in future research at improving skin permeation through transdermal delivery, associated with narrow therapeutic windows or low bioavailability of drugs with various health benefits.

8.
Colloids Surf B Biointerfaces ; 217: 112625, 2022 Sep.
Article in English | MEDLINE | ID: mdl-35738078

ABSTRACT

Inhaled crystalline silica causes inflammatory lung diseases, but the mechanism for its unique activity compared to other oxides remains unclear, preventing the development of potential therapeutics. Here, the molecular recognition mechanism between membrane epitopes and "nearly free silanols" (NFS), a specific subgroup of surface silanols, is identified and proposed as a novel broad explanation for particle toxicity in general. Silica samples having different bulk and surface properties, specifically different amounts of NFS, are tested with a set of membrane systems of decreasing molecular complexity and different charge. The results demonstrate that NFS content is the primary determinant of membrane disruption causing red blood cell lysis and changes in lipid order in zwitterionic, but not in negatively charged liposomes. NFS-rich silica strongly and irreversibly adsorbs zwitterionic self-assembled phospholipid structures. This selective interaction is corroborated by density functional theory and supports the hypothesis that NFS recognize membrane epitopes that exhibit a positive quaternary amino and negative phosphate group. These new findings define a new paradigm for deciphering particle-biomembrane interactions that will support safer design of materials and what types of treatments might interrupt particle-biomembrane interactions.


Subject(s)
Silanes , Silicon Dioxide , Epitopes , Silanes/chemistry , Silicon Dioxide/chemistry , Surface Properties
9.
Materials (Basel) ; 15(4)2022 Feb 12.
Article in English | MEDLINE | ID: mdl-35207897

ABSTRACT

This work reports for the first time a quantum mechanical study of the interactions of a model benzodiazepine drug, i.e., nitrazepam, with various models of amorphous silica surfaces, differing in structural and interface properties. The interest in these systems is related to the use of mesoporous silica as carrier in drug delivery. The adopted computational procedure has been chosen to investigate whether silica-drug interactions favor the drug degradation mechanism or not, hindering the beneficial pharmaceutical effect. Computed structural, energetics, and vibrational properties represent a relevant comparison for future experiments. Our simulations demonstrate that adsorption of nitrazepam on amorphous silica is a strongly exothermic process in which a partial proton transfer from the surface to the drug is observed, highlighting a possible catalytic role of silica in the degradation reaction of benzodiazepines.

10.
J Phys Chem C Nanomater Interfaces ; 126(4): 2243-2252, 2022 Feb 03.
Article in English | MEDLINE | ID: mdl-35145576

ABSTRACT

Phosphorus is an element of primary importance for all living creatures, being present in many biological activities in the form of phosphate (PO4 3-). However, there are still open questions about the origin of this specific element and on the transformation that allowed it to be incorporated in biological systems. The most probable source of prebiotic phosphorus is the intense meteoritic bombardment during the Archean era, a few million years after the solar system formation, which brought tons of iron-phosphide materials (schreibersite) on the early Earth crust. It was recently demonstrated that by simple wetting/corrosion processes from this material, various oxygenated phosphorus compounds are produced. In the present work, the wetting process of schreibersite (Fe2NiP) was studied by computer simulations using density functional theory, with the PBE functional supplemented with dispersive interactions through a posteriori empirical correction. To start disentangling the complexity of the system, only the most stable (110) surface of Fe2NiP was used simulating different water coverages, from which structures, water binding energies, and vibrational spectra have been predicted. The computed (ana-)harmonic infrared spectra have been compared with the experimental ones, thus, confirming the validity of the adopted methodology and models.

11.
Molecules ; 26(19)2021 Sep 28.
Article in English | MEDLINE | ID: mdl-34641423

ABSTRACT

Melatonin (MT) is a molecule of paramount importance in all living organisms, due to its presence in many biological activities, such as circadian (sleep-wake cycle) and seasonal rhythms (reproduction, fattening, molting, etc.). Unfortunately, it suffers from poor solubility and, to be used as a drug, an appropriate transport vehicle has to be developed, in order to optimize its release in the human tissues. As a possible drug-delivery system, ß-cyclodextrin (ßCD) represents a promising scaffold which can encapsulate the melatonin, releasing when needed. In this work, we present a computational study supported by experimental IR spectra on inclusion MT/ßCD complexes. The aim is to provide a robust, accurate and, at the same time, low-cost methodology to investigate these inclusion complexes both with static and dynamic simulations, in order to study the main actors that drive the interactions of melatonin with ß-cyclodextrin and, therefore, to understand its release mechanism.


Subject(s)
Computational Biology/methods , Drug Delivery Systems , Melatonin/metabolism , Molecular Dynamics Simulation , beta-Cyclodextrins/metabolism , Humans , Melatonin/chemistry , Solubility , beta-Cyclodextrins/chemistry
12.
J Chem Theory Comput ; 17(4): 2566-2574, 2021 Apr 13.
Article in English | MEDLINE | ID: mdl-33754704

ABSTRACT

Collagen proteins are spread in almost every vertebrate's tissue with mechanical function. The defining feature of this fundamental family of proteins is its well-known collagen triple-helical domain. This helical domain can have different geometries, varying in helical elongation and interstrands contact, as a function of the amino acidic composition. The helical geometrical features play an important role in the interaction of the collagen protein with cell receptors, but for the vast majority of collagen compositions, these geometrical features are unknown. Quantum mechanical (QM) simulations based on the density functional theory (DFT) provide a robust approach to characterize the scenario on the collagen composition-structure relationships. In this work, we analyze the role of the adopted computational method in predicting the collagen structure for two purposes. First, we look for a cost-effective computational approach to apply to a large-scale composition-structure analysis. Second, we attempt to assess the robustness of the predictions by varying the QM methods. Therefore, we have run geometry optimization on periodic models of the collagen protein using a variety of approaches based on the most commonly used DFT functionals (PBE, HSE06, and B3LYP) with and without dispersion correction (D3ABC). We have coupled these methods with several different basis sets, looking for the highest accuracy/cost ratio. Furthermore, we have studied the performance of the composite HF-3c method and the semiempirical GFN1-xTB method. Our results identify a computational recipe that is potentially capable of predicting collagen structural features in line with DFT simulations, with orders of magnitude reduced computational cost, encouraging further investigations on the topic.


Subject(s)
Collagen/chemistry , Density Functional Theory , Proteins/chemistry , Models, Molecular
13.
Cryst Growth Des ; 21(2): 897-907, 2021 Feb 03.
Article in English | MEDLINE | ID: mdl-33584152

ABSTRACT

We describe the energetic landscape beyond the solid-state dynamic behavior of a cyclic hexapeptoid decorated with four propargyl and two methoxyethyl side chains, namely, cyclo-(Nme-Npa2)2, Nme = N-(methoxyethyl)glycine, Npa = N-(propargyl)glycine. By increasing the temperature above 40 °C, the acetonitrile solvate form 1A starts to release acetonitrile molecules and undergoes a reversible single crystal-to-single crystal transformation into crystal form 1B with a remarkable conformational change in the macrocycle: two propargyl side chains move by 113° to form an unprecedented "CH-π zipper". Then, upon acetonitrile adsorption, the "CH-π zipper" opens and the crystal form 1B transforms back to 1A. By conformational energy and lattice energy calculations, we demonstrate that the dramatic side-chain movement is a peculiar feature of the solid-state assembly and is determined by a backbone conformational change that leads to stabilizing CH···OC backbone-to-backbone interactions tightening the framework upon acetonitrile release. Weak interactions as CH···OC and CH-π bonds with the guest molecules are able to reverse the transformation, providing the energy contribution to unzip the framework. We believe that the underlined mechanism could be used as a model system to understand how external stimuli (as temperature, humidity, or volatile compounds) could determine conformational changes in the solid state.

14.
Phys Chem Chem Phys ; 19(36): 25071-25079, 2017 Sep 20.
Article in English | MEDLINE | ID: mdl-28879366

ABSTRACT

A combination of experimental and computational techniques has been used to fully describe the thermodynamic properties and phase diagrams of the LiBH4-NaBH4-KBH4 system. The Calphad method was used to assess the thermodynamic properties of LiBH4-NaBH4, LiBH4-KBH4, and NaBH4-KBH4 binary systems and to extend the investigation to the LiBH4-NaBH4-KBH4 ternary system. Samples with various compositions in the ternary system were synthesised, both by ball milling and manual mixing of the parent borohydrides, and their thermal stability has been studied using in situ synchrotron radiation X-ray diffraction as a function of temperature and using differential scanning calorimetry. From collected experimental and literature data, a thermodynamic assessment of the ternary system led to the determination of the phase diagrams. In all cases, the solid solutions can be described in the frame of the regular solution model, with interaction parameters positive or equal to zero (i.e. ideal solution). In contrast, the liquid phase was described using negative interaction parameters. A new ternary eutectic composition was estimated and it was confirmed experimentally to be equal to a molar fraction of 0.66LiBH4-0.11NaBH4-0.23KBH4 with a melting temperature of 102 °C.

15.
Phys Chem Chem Phys ; 19(11): 7793-7806, 2017 Mar 15.
Article in English | MEDLINE | ID: mdl-28262865

ABSTRACT

A density functional theory (PBE functional) investigation is carried out, in which a model of an amorphous silica surface is functionalized by ortho-benzoquinone. Surface functionalization with catechol and quinone-based compounds is relevant in biomedical fields, from prosthetic implants to dentistry, to develop multifunctional coatings with antimicrobial properties. The present study provides atomistic information on the specific interactions between the functionalizing agent and the silanol groups at the silica surface. The distinct configurations of the functional groups, the hydrogen bond pattern, the role of dispersion forces and the simulated IR spectra provide detailed insight into the features of this model surface coating. Ab initio molecular dynamics gives further insights into the mobility of the functionalizing groups. As a final step, we studied the condensation reaction with allylamine, via Schiff base formation, to ground subsequent simulations on condensation with model peptides of antimicrobial activity.


Subject(s)
Molecular Dynamics Simulation , Quinones/chemistry , Silicon Dioxide/chemistry , Antimicrobial Cationic Peptides/chemistry , Hydrogen Bonding , Schiff Bases/chemistry , Spectrophotometry, Infrared , Surface Properties , Thermodynamics
16.
J Chem Theory Comput ; 13(1): 370-379, 2017 01 10.
Article in English | MEDLINE | ID: mdl-27976574

ABSTRACT

We studied the sensitivity of the energetic and geometrical features of the proline ring (pyrrolidine) to the quantum mechanical computational approach by adopting the proline monomer, trimer, and polymer, as simplified collagen protein models. Within the Density Functional Theory (DFT) approach, we tested the ability of different functionals (GGA PBE and the hybrid B3LYP), added with a posteriori empirical dispersion corrections (D), to predict the conformational potential energy surface of the five-membered heterocycle pyrrolidine ring for the above models, dictating the collagen main features. We also compared the DFT-D results with those from the recently proposed cost-effective HF-3c method and our variant HF-3c-027, both based on Hartree-Fock Hamiltonian and Gaussian minimal basis set properly corrected for basis set superposition error, structure deficiencies, and dispersion interactions. We found that dispersion interactions are essential to destabilize specific conformers. While the HF-3c and its HF-3c-027 variant are unreliable to predict accurately the energy of the ring conformers, structures are accurate. Indeed, the cost-effective DFT-D//HF-3c-027 approach in which the energetic is from the accurate DFT-D method on HF-3c-027 structures provides energetic in line with that derived by the costly DFT-D//DFT-D approach, paving the way to simulate more realistic collagen models of much larger size. The adoption of either PBE or B3LYP functional for the electronic part of the DFT-D method gives very similar results, recommending the first as the most cost-effective method for simulating large collagen models. The predicted most stable conformation computed for the periodic poly proline (type II) model allows for a higher flexibility, in agreement with experimental studies on collagen protein. The present results open the way to large-scale calculations of the collagen/hydroxyapatite system, crucial for understanding the atomistic details in bones and teeth.


Subject(s)
Models, Molecular , Peptides/chemistry , Molecular Conformation , Thermodynamics
17.
J Chem Theory Comput ; 12(7): 3340-52, 2016 Jul 12.
Article in English | MEDLINE | ID: mdl-27304925

ABSTRACT

A comparative assessment of the accuracy of different quantum mechanical methods for evaluating the structure and the cohesive energy of molecular crystals is presented. In particular, we evaluate the performance of the semiempirical HF-3c method in comparison with the B3LYP-D* and the Local MP2 (LMP2) methods by means of a fully periodic approach. Three benchmark sets have been investigated: X23, G60, and the new K7; for a total of 82 molecular crystals. The original HF-3c method performs well but shows a tendency at overbinding molecular crystals, in particular for weakly bounded systems. For the X23 set, the mean absolute error for the cohesive energies computed with the HF-3c method is comparable to the LMP2 one. A refinement of the HF-3c has been attempted by tuning the dispersion term in the HF-3c energy. While the performance on cohesive energy prediction slightly worsens, optimized unit cell volumes are in excellent agreement with experiment. Overall, the B3LYP-D* method combined with a TZP basis set gives the best results. For cost-effective calculations on molecular crystals, we propose to compute cohesive energies at the B3LYP-D*/TZP level of theory on the dispersion-scaled HF-3c optimized geometries (i.e., B3LYP-D*/TZP//HF-3c(0.27) also dubbed as SP-B3LYP-D*). Besides, for further benchmarking on molecular crystals, we propose to combine the three test sets in a new one denoted as MC82.

18.
Chem Sci ; 7(2): 1496-1507, 2016 Feb 01.
Article in English | MEDLINE | ID: mdl-29899894

ABSTRACT

Molecular simulations of proteins have been usually accomplished through empirical or semi-empirical potentials, due to the large size and inherent complexity of these biological systems. On the other hand, a theoretical description of proteins based on quantum-mechanical methods would however provide an unbiased characterization of their electronic properties, possibly offering a link between these and the ultimate biological activity. Yet, such approaches have been historically hindered by the large amount of requested computational power. Here we demonstrate the feasibility of periodic all-electron density functional theory calculations in the description of the crystal of the protein crambin (46 aminoacids), which is determined with exceptional structural accuracy. We have employed the hybrid B3LYP functional, coupled to an empirical description of London interactions (D*) to simulate the crambin crystal with an increasing amount of lattice water molecules in the cell (up to 172H2O per cell). The agreement with the experiment is good for both protein geometry and protein-water interactions. The energetics was computed to predict crystal formation energies, protein-water and protein-protein interaction energies. We studied the role of dispersion interactions which are crucial for holding the crambin crystal in place. B3LYP-D* electrostatic potential and dipole moment of crambin as well as the electronic charge flow from crambin to the solvating water molecules (0.0015e per H2O) have also been predicted. These results proved that quantum-mechanical simulations of small proteins, both free and in their crystalline state, are now feasible in a reasonable amount of time, by programs capable of exploiting high performance computing architectures, allowing the study of protein properties not easily amenable through classical force fields.

19.
Langmuir ; 31(23): 6321-31, 2015 Jun 16.
Article in English | MEDLINE | ID: mdl-26010674

ABSTRACT

In silico modeling of acidic (CH2COOH) or basic (CH2NH2) functionalized silica surfaces has been carried out by means of a density functional approach based on a gradient-corrected functional to provide insight into the characterization of experimentally functionalized surfaces via a plasma method. Hydroxylated surfaces of crystalline cristobalite (sporting 4.8 OH/nm(2)) mimic an amorphous silica interface as unsubstituted material. To functionalize the silica surface we transformed the surface Si-OH groups into Si-CH2COOH and Si-CH2NH2 moieties to represent acidic/basic chemical character for the substitution. Structures, energetics, electronic, and vibrational properties were computed and compared as a function of the increasing loading of the functional groups (from 1 to 4 per surface unit cell). Classical molecular dynamics simulations of selected cases have been performed through a Reax-FF reactive force field to assess the mobility of the surface added chains. Both DFT and force field calculations identify the CH2NH2 moderate surface loading (1 group per unit cell) as the most stable functionalization, at variance with the case of the CH2COOH group, where higher loadings are preferred (2 groups per unit cell). The vibrational fingerprints of the surface functionalities, which are the ν(C═O) stretching and δ(NH2) bending modes for acidic/basic cases, have been characterized as a function of substitution percentage in order to guide the assignment of the experimental data. The final results highlighted the different behavior of the two types of functionalization. On the one hand, the frequency associated with the ν(C═O) mode shifts to lower wavenumbers as a function of the H-bond strength between the surface functionalities (both COOH and SiOH groups), and on the other hand, the δ(NH2) frequency shift seems to be caused by a subtle balance between the H-bond donor and acceptor abilities of the NH2 moiety. Both sets of data are in general agreement with experimental measurements on the corresponding silica-functionalized materials and provide finer details for a deeper interpretation of experimental spectra.


Subject(s)
Electrons , Silicon Dioxide/chemistry , Water/chemistry , Acids , Adsorption , Alkalies , Hydroxylation , Molecular Dynamics Simulation , Quantum Theory , Surface Properties , Thermodynamics , Vibration
20.
J Phys Chem A ; 118(31): 5801-7, 2014 Aug 07.
Article in English | MEDLINE | ID: mdl-24467179

ABSTRACT

Silica-based materials find applications as excipients and, particularly for those of mesoporous nature, as drug delivery agents for pharmaceutical formulations. Their performance can be crucially affected by water moisture, as it can modify the behavior of these formulations, by limiting their shelf life. Here we describe the role of water microsolvation on the features of ibuprofen adsorbed on a model of amorphous silica surface by means of density functional theory (DFT) simulations. Starting from the results of the simulation of ibuprofen in interaction with a dry hydrophobic amorphous silica surface, a limited number of water molecules has been added to study the configurational landscape of the microsolvated system. Structural and energetics properties, as well as the role of dispersive forces, have been investigated. Our simulations have revealed that the silica surface exhibits a higher affinity for water than for ibuprofen, even if several structures coexist at room temperature, with an active competition of ibuprofen and water for the exposed surface silanols. Dispersive interactions play a key role in this system, as pure DFT fails to correctly describe its potential energy surface. Indeed, van der Waals forces are the leading contribution to adsorption, independently of whether the drug is hydrogen-bonded directly to the surface or via water molecules.


Subject(s)
Ibuprofen/chemistry , Silicon Dioxide/chemistry , Water/chemistry , Adsorption , Computer Simulation , Hydrogen Bonding , Hydrophobic and Hydrophilic Interactions , Microfluidics , Models, Chemical , Solvents/chemistry , Surface Properties
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